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Array CGH identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas.

Lassmann S, Weis R, Makowiec F, Roth J, Danciu M, Hopt U, Werner M.

J Mol Med (Berl). 2007 Mar;85(3):293-304. Epub 2006 Dec 2.


Comparison of sample preparation methods for ChIP-chip assays.

O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ.

Biotechniques. 2006 Nov;41(5):577-80.


Specific recognition of ZNF217 and other zinc finger proteins at a surface groove of C-terminal binding proteins.

Quinlan KG, Nardini M, Verger A, Francescato P, Yaswen P, Corda D, Bolognesi M, Crossley M.

Mol Cell Biol. 2006 Nov;26(21):8159-72. Epub 2006 Aug 28.


GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.


Suz12 binds to silenced regions of the genome in a cell-type-specific manner.

Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ.

Genome Res. 2006 Jul;16(7):890-900. Epub 2006 Jun 2.


Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.

Bieda M, Xu X, Singer MA, Green R, Farnham PJ.

Genome Res. 2006 May;16(5):595-605. Epub 2006 Apr 10.


Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis.

Scacheri PC, Davis S, Odom DT, Crawford GE, Perkins S, Halawi MJ, Agarwal SK, Marx SJ, Spiegel AM, Meltzer PS, Collins FS.

PLoS Genet. 2006 Apr;2(4):e51. Epub 2006 Apr 7.


C-terminal binding proteins: emerging roles in cell survival and tumorigenesis.

Bergman LM, Blaydes JP.

Apoptosis. 2006 Jun;11(6):879-88. Review.


ZNF217 suppresses cell death associated with chemotherapy and telomere dysfunction.

Huang G, Krig S, Kowbel D, Xu H, Hyun B, Volik S, Feuerstein B, Mills GB, Stokoe D, Yaswen P, Collins C.

Hum Mol Genet. 2005 Nov 1;14(21):3219-25. Epub 2005 Oct 3.


Core transcriptional regulatory circuitry in human embryonic stem cells.

Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA.

Cell. 2005 Sep 23;122(6):947-56.


Regulation of LSD1 histone demethylase activity by its associated factors.

Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y.

Mol Cell. 2005 Sep 16;19(6):857-64.


An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation.

Lee MG, Wynder C, Cooch N, Shiekhattar R.

Nature. 2005 Sep 15;437(7057):432-5. Epub 2005 Aug 3.


Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.

Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M.

Cell. 2005 Jul 15;122(1):33-43.


CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome.

Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD.

Nucleic Acids Res. 2005 May 23;33(9):2952-61. Print 2005.


Gene copy number change events at chromosome 20 and their association with recurrence in gastric cancer patients.

Yang SH, Seo MY, Jeong HJ, Jeung HC, Shin J, Kim SC, Noh SH, Chung HC, Rha SY.

Clin Cancer Res. 2005 Jan 15;11(2 Pt 1):612-20.


Sequential DNA methylation of the Nanog and Oct-4 upstream regions in human NT2 cells during neuronal differentiation.

Deb-Rinker P, Ly D, Jezierski A, Sikorska M, Walker PR.

J Biol Chem. 2005 Feb 25;280(8):6257-60. Epub 2004 Dec 21.


Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.

Pavesi G, Mereghetti P, Mauri G, Pesole G.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203.


Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR.

Cell. 2004 Feb 20;116(4):499-509.


High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays.

Oberley MJ, Tsao J, Yau P, Farnham PJ.

Methods Enzymol. 2004;376:315-34. Review. No abstract available.


Distribution of NF-kappaB-binding sites across human chromosome 22.

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Epub 2003 Oct 3.

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